Fig. 2

LUSTR is robust in tests with simulated libraries. To test the performance of LUSTR in size and allele fraction estimations, we generated simulated reads from C9orf72 locus including 2X1000bp flanking regions and the repeats of (a) homozygous alleles with different expanded or contracted repeat sizes (ranging from -10.3 to + 1000), and (b) heterozygous alleles with one reference allele and one expanded allele (+ 100 repeats), mixed by different fractions. Reads 150 nucleotides in length were generated in pairs with an error rate of 0.5% including mismatches, insertions, and deletions, under different average coverage ranging from 1 to 100X. Each combination was repeated 10 times as a group. The number of failed libraries in each group, which were due to low coverage and mainly for 1X coverage condition, is indicated by red shade. For successfully called libraries, we examined the estimated repeat size variants (a) and then estimated the fraction of the reference allele (b). The observed and expected are shown for each scenario evaluated. We compared the average result in each group (indicated by a black solid line) with the expectation (indicated by a blue dotted line) and calculated the square of correlation coefficient (r²). Among the sizes evaluated, we specifically tested the repeat size variations for the deletion allele (-10.3), reference allele (0), and allele with repeat sizes close to reads length (+ 15) in Fig. 2a. For size estimation (a), LUSTR showed robust performance starting from 5X coverage and became very close to the expectations from as low as only 10X coverage. For fraction estimation (b) LUSTR required higher coverage, but still exhibited reliable estimates showing the expected allelic ratio with only 10X coverage. This result showed that LUSTR robustly infers both repeat size and allele fraction estimations even for low coverage libraries